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Design of a Low-Cost, Submersible, Digital Holographic Microscope for in Situ Microbial Imaging

The methodologies for studying marine microbiology typically consist of utilizing instrumentation within a laboratory. This typically requires extracting a sample from its place of origin prior to examination, which may be days after collection. Oftentimes, the solution is to bring the lab to the ocean, which may be costly and provide further limitations for a sterile and stable laboratory environment. Here we present a low-cost, submersible, digital holographic microscope (DHM) designed to image marine microorganisms (such as bacteria and plankton) in their natural underwater environment. Our instrument eliminates the need to transport samples and allows for instantaneous data collection of microbes in-situ. The DHM achieves sub-micron spatial resolution and is paired with artificial intelligence for the detection and tracking of specimens to reduce the overall collected data. This instrument also aims to reduce the cost of manufacturing and field expenses relative to marine microbiological research. “Off the shelf” components were selected in the design process of this instrument which allows us to achieve precise results without sacrificing data quality. The DHM itself costs under one thousand dollars and features a low-cost high-resolution camera, the Arducam MT9J001. Included in the design were five main subsystems: optical, mechanical, electrical, power, and machine learning. Our on board computer and artificial intelligence consist of a Raspberry Pi 4 (8 Gb) and Google Coral USB Tensorflow accelerator. Instrument testing has successfully proven our abilities of data acquisition for at least two hours in depths of at least forty meters below sea level. Additionally, our artificial intelligence system is currently capable of tracking up to ten areas of interest in a fraction of a second with over ninety percent confidence via the neural net driven by the tensor cores on the Google Coral. Furthermore, we have demonstrated the versatility of our instrument by mounting it on an ocean-going ROV, the BlueRov2 by BlueRobotics. Our tests on the BlueRov2 exemplified the cost-effective nature of a submersible and reusable instrument that can be implemented in moderate environments and on most vessels.

Wallace, James Kent↗

The Topology of Symmetric Tensor Fields

Combinatorial topology, also known as "rubber sheet geometry", has extensive applications in geometry and analysis, many of which result from connections with the theory of differential equations. A link between topology and differential equations is vector fields. Recent developments in scientific visualization have shown that vector fields also play an important role in the analysis of second-order tensor fields. A second-order tensor field can be transformed into its eigensystem, namely, eigenvalues and their associated eigenvectors without loss of information content. Eigenvectors behave in a similar fashion to ordinary vectors with even simpler topological structures due to their sign indeterminacy. Incorporating information about eigenvectors and eigenvalues in a display technique known as hyperstreamlines reveals the structure of a tensor field. The simplify and often complex tensor field and to capture its important features, the tensor is decomposed into an isotopic tensor and a deviator. A tensor field and its deviator share the same set of eigenvectors, and therefore they have a similar topological structure. A a deviator determines the properties of a tensor field, while the isotopic part provides a uniform bias. Degenerate points are basic constituents of tensor fields. In 2-D tensor fields, there are only two types of degenerate points; while in 3-D, the degenerate points can be characterized in a Q'-R' plane. Compressible and incompressible flows share similar topological feature due to the similarity of their deviators. In the case of the deformation tensor, the singularities of its deviator represent the area of vortex core in the field. In turbulent flows, the similarities and differences of the topology of the deformation and the Reynolds stress tensors reveal that the basic addie-viscosity assuptions have their validity in turbulence modeling under certain conditions.

Levin, Yingmei↗

Polar wander of an ice shell on Europa

The present consideration of a hypothesized ice shell around Europa, which is decoupled from the silicate core by a liquid water layer and possesses a spatially varying thermal equilibrium thickness profile, proceeds through the development of equations for variations in the inertia tensor of a body when second-harmonic-degree topography is added to the crustal base. Attention is given to a realistic model in which the shell and ocean are assumed to undergo reorientations as a single entity independently of the core, but subject to viscous dissipation within the shell. Shell friction is in this case noted to preclude polar wander, unless a low conductivity regolith increases the near-surface temperature by a few tens of degrees C; the ice beneath the regolith would then behave viscously on the time-scale of polar wander.

Ojakangas, Gregory W.↗

Turbulence Measurements in the Near Field of a Wingtip Vortex

The roll-up of a wingtip vortex, at Reynolds number based on chord of 4.6 million was studied with an emphasis on suction side and near wake measurements. The research was conducted in a 32 in. x 48 in. low-speed wind tunnel. The half-wing model had a semi-span of 36 in. a chord of 48 in. and a rounded tip. Seven-hole pressure probe measurements of the velocity field surrounding the wingtip showed that a large axial velocity of up to 1.77 U(sub infinity) developed in the vortex core. This level of axial velocity has not been previously measured. Triple-wire probes have been used to measure all components of the Reynolds stress tensor. It was determined from correlation measurements that meandering of the vortex was small and did not appreciably contribute to the turbulence measurements. The flow was found to be turbulent in the near-field (as high as 24 percent RMS w - velocity on the edge of the core) and the turbulence decayed quickly with streamwise distance because of the nearly solid body rotation of the vortex core mean flow. A streamwise variation of the location of peak levels of turbulence, relative to the core centerline, was also found. Close to the trailing edge of the wing, the peak shear stress levels were found at the edge of the vortex core, whereas in the most downstream wake planes they occurred at a radius roughly equal to one-third of the vortex core radius. The Reynolds shear stresses were not aligned with the mean strain rate, indicating that an isotropic-eddy-viscosity based prediction method cannot accurately model the turbulence in the cortex. In cylindrical coordinates, with the origin at the vortex centerline, the radial normal stress was found to be larger than the circumferential.

Chow, Jim↗

Some new results on spherical dynamos

Small-scale motions in the earth's liquid core are likely to be highly anisotropic because of the effects of rotation. Guided by physical considerations, the 'alpha-effect' described by an anisotropic tensor alpha sub ik is formulated and the corresponding boundary value problem for a sphere is solved for a variety of boundary conditions. A converged solution has been obtained only in the case of the Fermi condition of an infinitely conducting exterior of the sphere. Some remarks are made on the hypothetical upper bound on magnetic field strengths in planetary cores originally proposed by Busse (1976).

Busse, F. H.↗

Uncertainties for two-dimensional models of solar rotation from helioseismic eigenfrequency splitting

Observed solar p-mode frequency splittings can be used to estimate angular velocity as a function of position in the solar interior. Formal uncertainties of such estimates depend on the method of estimation (e.g., least-squares), the distribution of errors in the observations, and the parameterization imposed on the angular velocity. We obtain lower bounds on the uncertainties that do not depend on the method of estimation; the bounds depend on an assumed parameterization, but the fact that they are lower bounds for the 'true' uncertainty does not. Ninety-five percent confidence intervals for estimates of the angular velocity from 1986 Big Bear Solar Observatory (BBSO) data, based on a 3659 element tensor-product cubic-spline parameterization, are everywhere wider than 120 nHz, and exceed 60,000 nHz near the core. When compared with estimates of the solar rotation, these bounds reveal that useful inferences based on pointwise estimates of the angular velocity using 1986 BBSO splitting data are not feasible over most of the Sun's volume. The discouraging size of the uncertainties is due principally to the fact that helioseismic measurements are insensitive to changes in the angular velocity at individual points, so estimates of point values based on splittings are extremely uncertain. Functionals that measure distributed 'smooth' properties are, in general, better constrained than estimates of the rotation at a point. For example, the uncertainties in estimated differences of average rotation between adjacent blocks of about 0.001 solar volumes across the base of the convective zone are much smaller, and one of several estimated differences we compute appears significant at the 95% level.

Genovese, Christopher R.↗

ELAS: A general-purpose computer program for the equilibrium problems of linear structures. Volume 2: Documentation of the program

A general purpose digital computer program for the in-core solution of linear equilibrium problems of structural mechanics is documented. The program requires minimum input for the description of the problem. The solution is obtained by means of the displacement method and the finite element technique. Almost any geometry and structure may be handled because of the availability of linear, triangular, quadrilateral, tetrahedral, hexahedral, conical, triangular torus, and quadrilateral torus elements. The assumption of piecewise linear deflection distribution insures monotonic convergence of the deflections from the stiffer side with decreasing mesh size. The stresses are provided by the best-fit strain tensors in the least squares at the mesh points where the deflections are given. The selection of local coordinate systems whenever necessary is automatic. The core memory is used by means of dynamic memory allocation, an optional mesh-point relabelling scheme and imposition of the boundary conditions during the assembly time.

Utku, S.↗

Near-wall reconstruction of higher order moments and length scales using the POD

An analysis of the near-wall behavior of the proper orthogonal decomposition (POD) eigenfunctions derived from direct numerical simulation (DNS) of channel flow is performed. Consistent with previous studies, a low order multi-mode reconstruction of the kinetic energy and Reynolds shear stress suffices. A similar reconstruction of the isotropic dissipation rate is shown to be insufficient, however. An analysis is performed of the multi-mode composition of the dissipation rate in the near-wall region, and it is shown that a significant number of higher-order modes are required to achieve the correct asymptotic consistency in the near-wall region. In an attempt to avoid this problem, a length scale definition is proposed in terms of an integration of the correlation tensor which factors in the presence of the wall. The wall is accounted for by only integrating out to 2y(+) and not over the entire domain. Viscous and inviscid estimates for the dissipation were used in the near-wall and core regions respectively, in conjunction with this length scale representation to obtain an estimate of the dissipation throughout the domain. The resulting dissipation exhibits the proper behavior near the wall and in the inertial layer. A 1 POD mode estimate of the length scale is computed and found to agree quite well with the length scale obtained when the entire correlation tensor is used.

Glauser, Mark N.↗

Spectral Characteristics of Wake Vortex Sound During Roll-Up

This report presents an analysis of the sound spectra generated by a trailing aircraft vortex during its rolling-up process. The study demonstrates that a rolling-up vortex could produce low frequency (less than 100 Hz) sound with very high intensity (60 dB above threshold of human hearing) at a distance of 200 ft from the vortex core. The spectrum then drops o rapidly thereafter. A rigorous analytical approach has been adopted in this report to derive the spectrum of vortex sound. First, the sound pressure was solved from an alternative treatment of the Lighthill s acoustic analogy approach [1]. After the application of Green s function for free space, a tensor analysis was applied to permit the removal of the source term singularity of the wave equation in the far field. Consequently, the sound pressure is expressed in terms of the retarded time that indicates the time history and spacial distribution of the sound source. The Fourier transformation is then applied to the sound pressure to compute its spectrum. As a result, the Fourier transformation greatly simplifies the expression of the vortex sound pressure involving the retarded time, so that the numerical computation is applicable with ease for axisymmetric line vortices during the rolling-up process. The vortex model assumes that the vortex circulation is proportional to the time and the core radius is a constant. In addition, the velocity profile is assumed to be self-similar along the aircraft flight path, so that a benchmark vortex velocity profile can be devised to obtain a closed form solution, which is then used to validate the numerical calculations for other more realistic vortex profiles for which no closed form solutions are available. The study suggests that acoustic sensors operating at low frequency band could be profitably deployed for detecting the vortex sound during the rolling-up process.

Booth, Earl R., Jr.↗

Cold dissipationless collapse of spherical systems - Sensitivity to the initial density law

The collapse of cold, initially spherical systems with varying degrees of central condensation is investigated. The way in which the final shape of a collapsing system depends on the initial density law is examined. For an initial stellar number density rho varies as r exp -n, where n is in the range 0-2.5, the final, nearly prolate shape is given by a/c is approximately equal to 1.28(1 + 0.16 n), where a/c is the ratio of long to short axes of the inertia ellipsoid computed from the moment of inertia tensor of the most tightly bound 80 percent of the mass. The properties associated with the final states in the present computations are also studied. The collapsing systems develop an anisotropic halo dominated by radial orbits surrounding an isotropic core as predicted by Burkert (1990).

Cannizzo, John K.↗

Redistribution of resonance radiation. II - The effect of magnetic fields.

Previously obtained results for scattering of radiation in the presence of collisions are restated in a density matrix formalism which employs an irreducible-tensor description of the radiation field. This formalism is particularly useful for problems associated with radiative transfer theory. The redistribution is then extended to include the effect of a weak magnetic field. By averaging over a finite bandwidth which is on the order of the Doppler width, simplified expressions of physical significance for the scattering in the Doppler core and the Lorentz wings are obtained. Expressions are also obtained for the corresponding source function of radiative transfer theory.

Omont, A.↗

Second moment closure analysis of the backstep flow database

A Second Moment Closure computation (SMC) is compared in detail with the Direct Numerical Simulation (DNS) data of Le and Moin for the backstep flow at Re = 5,000 in an attempt to understand why the intensity of the backflow and, consequently, the friction coefficient in the recirculation bubble are severely underestimated. The data show that this recirculation bubble is far from being laminar except in the very near wall layer. A novel 'differential a priori' procedure was used, in which the full transport equation for one isolated component of the Reynolds stress tensor was solved using DNS data as input. Conclusions are then different from what would have been deduced by comparing a full simulation to a DNS. One cause of discrepancy was traced back to insufficient transfer of energy to the normal stress by pressure strain, but was not cured. A significant finding, confirmed by the DNS data in the core region of a channel flow, is that the coefficient that controls destruction of dissipation, C epsilon(sub 2), should be decreased by a factor of 2 when production is vanishing. This is also the case in the recirculation bubble, and a new formulation has cured 25% of the backflow discrepancy.

Parneix, S.↗

Automated Fluid Feature Extraction from Transient Simulations

In the past, feature extraction and identification were interesting concepts, but not required to understand the underlying physics of a steady flow field. This is because the results of the more traditional tools like iso-surfaces, cuts and streamlines were more interactive and easily abstracted so they could be represented to the investigator. These tools worked and properly conveyed the collected information at the expense of much interaction. For unsteady flow-fields, the investigator does not have the luxury of spending time scanning only one "snap-shot" of the simulation. Automated assistance is required in pointing out areas of potential interest contained within the flow. This must not require a heavy compute burden (the visualization should not significantly slow down the solution procedure for co-processing environments like pV3). And methods must be developed to abstract the feature and display it in a manner that physically makes sense. The following is a list of the important physical phenomena found in transient (and steady-state) fluid flow: (1) Shocks, (2) Vortex cores, (3) Regions of recirculation, (4) Boundary layers, (5) Wakes. Three papers and an initial specification for the (The Fluid eXtraction tool kit) FX Programmer's guide were included. The papers, submitted to the AIAA Computational Fluid Dynamics Conference, are entitled : (1) Using Residence Time for the Extraction of Recirculation Regions, (2) Shock Detection from Computational Fluid Dynamics results and (3) On the Velocity Gradient Tensor and Fluid Feature Extraction.

Haimes, Robert↗

The Spectral and Statistical Properties of Turbulence Generated by a Vortex/Blade-Tip Interaction

The perpendicular interaction of a streamwise vortex with the tip of a lifting blade was studied in incompressible flow to provide information useful to the accurate prediction of helicopter rotor noise and the understanding of vortex dominated turbulent flows. The vortex passed 0.3 chord lengths to the suction side of the blade tip, providing a weak interaction. Single and two-point turbulence measurements were made using sub-miniature four sensor hot-wire probes 15 chord lengths downstream of the blade trailing edge; revealing the mean velocity and Reynolds stress tensor distributions of the turbulence, as well as its spanwise length scales as a function of frequency. The single point measurements show the flow downstream of the blade to be dominated by the interaction of the original tip vortex and the vortex shed by the blade. These vortices rotate about each other under their mutual induction, winding up the turbulent wakes of the blades. This interaction between the vortices appears to be the source of new turbulence in their cores and in the region between them. This turbulence appears to be responsible for some decay in the core of the original vortex, not seen when the blade is removed. The region between the vortices is not only a region of comparatively large stresses, but also one of intense turbulence production. Velocity autospectra measured near its center suggests the presence quasi-periodic large eddies with axes roughly parallel to a line joining the vortex cores. Detailed two-point measurements were made on a series of spanwise cuts through the flow so as to reveal the turbulence scales as they would be seen along the span of an intersecting airfoil. The measurements were made over a range of probe separations that enabled them to be analyzed not only in terms of coherence and phase spectra but also in terms of wave-number frequency (kappa-omega) spectra, computed by transforming the measured cross-spectra with respect to the spanwise separation of the probes. These data clearly show the influence of the coherent eddies in the spiral wake and the turbulent region between the cores. These eddies produce distinct peaks in the upwash velocity kappa-omega spectra, and strong anisotropy manifested both in the decay of the kappa-omega spectrum at larger wave-numbers and in differences between the kappa-omega spectra of different components. None of these features are represented in the von Karman spectrum for isotropic turbulence that is often used in broadband noise computations. Wave-number frequency spectra measured in the cores appear to show some evidence that the turbulence outside sets tip core waves, as has previously been hypothesized. These spectra also provide for the first time a truly objective method for distinguishing velocity fluctuations produced by core wandering from other motions.

Devenport, William J.↗

Frequency dependence of coherent structures in a Mach number 0.6 jet

The existence of a large scale structure in a Mach number 0.6, axisymmetric jet of cold air has been proven by previous work. In order to further characterize the coherent structure, phase averaged measurements of the axial mass velocity, radial velocity, and one component of the Reynolds stress tensor were made. These measured values were compared to the total fluctuation levels for each quantity and the result expressed as a percent of the total fluctuation level contained in the organized structure at Strouhal numbers of 0.16, 0.32, 0.474, 0.95, and 1.26. All of the phase averaged measurements required that the jet be artificially excited. The fluctuation profiles showed that the axial mass velocity fluctuations maximized when excited at a Strouhal number of 0.474. The radial velocity fluctuations possessed a lower amplitude for both the full wave and phase averaged fluctuations than the axial mass velocity fluctuation. The Reynolds stress decayed faster than the other two quantities past the end of the potential core for both the full wave and phase averaged components. The coherence contours showed that the radial velocity fluctuations possessed higher levels of coherence than the axial mass velocity fluctuation and the Reynolds stress.

Morrison, G. L.↗

Organized kinetic energy backscatter in the hurricane boundary layer from radar measurements

The fluid mechanics of hurricanes strongly depends on boundary layer energetics due to the warm-core nature of the system with peak velocities located at lower levels. One barrier that has inhibited a more complete characterization of energy transfer in the boundary layer is a lack of observations that resolve large, turbulent eddies. In particular, the occurrence and structure of upscale energy transfer (backscatter) in the hurricane boundary layer as well as the effects of backscatter on the vortex intensity are unknown. The analysis presented here of very high-resolution, three-dimensional wind observations from Hurricane Rita (2005) at peak intensity reveals large regions of organized backscatter in the boundary layer associated with coherent, turbulent eddies. Strong forwardscatter is also found next to the backscatter regions due to the interaction between adjacent eddies. Two components of the stress tensor are primarily responsible for this alternating scatter structure, as shown by large correlation coefficients between the fields: the radial–vertical component (τ13) and the azimuthal–vertical component (τ23) with average correlations of 79% and 49 %, respectively. The Leonard, Reynolds and cross-term stress components are also provided. The impact of the sub-filter-scale energy transfer is estimated by computing the kinetic energy budget for the resolved-scale and eddy-scale motions. The results show that the sub-filter-scale energy transfer term is of the same order as the other terms in the eddy-scale budgets, contributing between 16% and 40% to the local time tendency with an average contribution of approximately 30 %. These results indicate that the coherent turbulent eddies can affect the vortex dynamics through wave–wave nonlinear interactions, which can subsequently influence the wave–mean flow interactions. This is the first study to examine the full sub-filter-scale

Sydney Sroka↗

Magnetospheric Multiscale (MMS) Mission Attitude Ground System Design

This paper describes the attitude ground system (AGS) design to be used for support of the Magnetospheric MultiScale (MMS) mission. The AGS exists as one component of the mission operations control center. It has responsibility for validating the onboard attitude and accelerometer bias estimates, calibrating the attitude sensors and the spacecraft inertia tensor, and generating a definitive attitude history for use by the science teams. NASA's Goddard Space Flight Center (GSFC) in Greenbelt, Maryland is responsible for developing the MMS spacecraft, for the overall management of the MMS mission, and for mission operations. MMS is scheduled for launch in 2014 for a planned two-year mission. The MMS mission consists of four identical spacecraft flying in a tetrahedral formation in an eccentric Earth orbit. The relatively tight formation, ranging from 10 to 400 km, will provide coordinated observations giving insight into small-scale magnetic field reconnection processes. By varying the size of the tetrahedron and the orbital semi-major axis and eccentricity, and making use of the changing solar phase, this geometry allows for the study of both bow shock and magnetotail plasma physics, including acceleration, reconnection, and turbulence. The mission divides into two phases for science; these phases will have orbit dimensions of l.2xl2 Earth radii in the first phase and l.2x25 Earth radii in the second in order to study the dayside magnetopause and the nightside magnetotail, respectively. The orbital periods are roughly one day and three days for the two mission phases. Each of the four MMS spacecraft will be spin stabilized at 3 revolutions per minute (rpm), with the spin axis oriented near the ecliptic north pole but tipped approximately 2.5 deg towards the Sun line. The main body of each spacecraft will be an eight-sided platform with diameter of 3.4 m and height of 1.2 m. Several booms are attached to this central core: two axial booms of 14.9 m length, two radial magnetometer booms of 5 m length, and four radial -wire booms of 60 m length. Attitude and orbit control will use a set of axial and radial thrusters. A four-head star tracker and a slit-type digital Sun sensor (DSS) provide input for attitude determination. In addition, an accelerometer will be· used for closed-loop orbit maneuver control. The primary AGS product will be a daily definitive attitude history. Due to power limitations; the star tracker and accelerometer data will not be available at all times. However, tracker data from at least 10 percent of each orbit and continuous DSS data will be provided. An extended Kalman filter (EKF) will be used to estimate the three-axis attitude (i.e., spin axis orientation and spin phase) and rotation rate for all times when the tracker data is valid. For other times, the attitude is generated by assuming a constant angular momentum vector in the inertial frame. The DSS sun pulse will provide a timing signal to maintain an accurate spin phase. There will be times when the Sun is occulted and DSS data is not available. If this occurs at the start or end of a definitive attitude product, then the spin phase will be extrapolated using the mean rate determined by the EKF.

Sedlak, Joseph E.↗

Magnetospheric Multiscale (MMS) Mission Attitude Ground System Design

This paper describes the attitude ground system (AGS) design to be used for support of the Magnetospheric MultiScale (MMS) mission. The AGS exists as one component of the mission operations control center. It has responsibility for validating the onboard attitude and accelerometer bias estimates, calibrating the attitude sensors and the spacecraft inertia tensor, and generating a definitive attitude history for use by the science teams. NASA's Goddard Space Flight Center (GSFC) in Greenbelt, Maryland is responsible for developing the MMS spacecraft, for the overall management of the MMS mission, and for mission operations. MMS is scheduled for launch in 2014 for a planned two-year mission. The MMS mission consists of four identical spacecraft flying in a tetrahedral formation in an eccentric Earth orbit. The relatively tight formation, ranging from 10 to 400 km, will provide coordinated observations giving insight into small-scale magnetic field reconnection processes. By varying the size of the tetrahedron and the orbital semi-major axis and eccentricity, and making use of the changing solar phase, this geometry allows for the study of both bow shock and magnetotail plasma physics, including acceleration, reconnection, and turbulence. The mission divides into two phases for science; these phases will have orbit dimensions of 1.2 x 12 Earth radii in the first phase and 1.2x25 Earth radii in the second in order to study the dayside magnetopause and the nightside magnetotail, respectively. The orbital periods are roughly one day and three days for the two mission phases. Each of the four MMS spacecraft will be spin stabilized at 3 revolutions per minute (rpm), with the spin axis oriented near the ecliptic north pole but tipped approximately 2.5 deg towards the Sun line. The main body of each spacecraft will be an eight-sided platform with diameter of 3.4 m and height of 1.2 m. Several booms are attached to this central core: two axial booms of 14.9 m length, two radial magnetometer booms of 5 m length, and four radial wire booms of 60 m length. Attitude and orbit control will use a set of axial and radial thrusters. A four-head star tracker and a slit-type digital Sun sensor (DSS) provide input for attitude determination. In addition, an accelerometer will be used for closed-loop orbit maneuver control. The primary AGS product will be a daily definitive attitude history. Due to power limitations, the star tracker and accelerometer data will not be available at all times. However, tracker data from at least 10 percent of each orbit and continuous DSS data will be provided. An extended Kalman filter (EKF) will be used to estimate the three-axis attitude (i.e., spin axis orientation and spin phase) and rotation rate for all times when the tracker data is valid. For other times, the attitude is generated by assuming a constant angular momentum vector in the inertial frame. The DSS sun pulse will provide a timing signal to maintain an accurate spin phase. There will be times when the Sun is occulted and DSS data is not available. If this occurs at the start or end of a definitive attitude product, then the spin phase will be extrapolated using the mean rate determined by the EKF.

Sedlak, Joseph E.↗